JOSS review - demo jupyter notebook

[KatyBrown]

Issue raised as part of the JOSS review process to address the "Functionality" check https://github.com/openjournals/joss-reviews/issues/6869

In the demo Jupyter notebook, some of the commands do not work with the version of the code currently on pip - I think the final three functions in fraggler.py - fit_ladder, find_peaks and fit_area must be elsewhere in that version as there are ImportErrors for these functions.

I therefore cloned the git repo directly and imported fraggler.fraggler from the cloned folder but this led to different errors - I would guess that the fraggler.FsaFile function has some different parameters in the current version of the code on GitHub than in the tutorial, as it expected sample_channel, min_distance_between_peaks and min_size_standard_height to be specified but they are not in the notebook, and it didn't recognise trace_channel.

I didn't progress past that point but it seems like the tutorial for the Python version of the code needs updating to be usable.

[kdm9]

Additionally, the link to tutorial.ipynb in the paper is broken (points to root of repo, not to the demo dir).

[willros]

Hi @KatyBrown and @kdm9!

I have updated the version of fraggler on pypi. The tutorial works for me when I pip install the latest version of fraggler. Try it out and let me know if it still does not work.

William

[KatyBrown]

Thank you, the tutorial works nicely now.